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The standard distribution format for ROS packages on Ubuntu is binaries (debs), and the install into /opt/ros/<distro>. rosdep can find and install these for you, along with installing any normal ubuntu packages that might be required as dependencies.
You cannot and should not attempt to modify the installed binary packages.
If you want to modify a package or see how it works, you should go to the package's wiki page, download the source code to your workspace, and modify and build it there. Any package that you have installed in your workspace will override (shadow) a binary package with the same name, so you don't have to worry about uninstalling binary packages. (This process is call overlaying).
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